title: shScr1-11d

status: Public on Dec 28 2020

city: West Lafayette

first: Emily

last: Dykhuizen

state: IN

address: 201 S. University

department: medicinal chemistry and molecular pharmacology

institute: Purdue University

data_processing:
Data quality control and filtering was performed with Trim Galore.
Read-mapping against the human (hg19) genome was performed with STAR.
Raw read counts for each gene from each replicate were determined using HTSeq.
Differential expression analysis was performed with R-package edgeR .
Genome_build: Hg19
Supplementary_files_format_and_content: tab delimited txt file include raw counts, FPKM and log2FC values.

source_name: LNCaP cells

growth_protocol: LNCaP prostate cancer cell lines were grown under normal conditions: RPMI with 10% FBS

extract_protocol:
RNA was isolated from cells using Trizol® and following manufacturer's recommendations. RNA was further purified using Qiagen Rneasy kit.
Libraries were constructed using Ovation® Ultralow V2 DNA-Seq Library Preparation Kit from Tecan, according the manufacturer's instructions

treatment_protocol: knockouts and knockdowns were generated using lentiviral mediated CRISPR-Cas9.

tag: cell type

value: LNCaP

tag: genetic manipulation

value: lentivirus with shScrambled

value: 11d of lentivirus


title: shScr2-11d

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: treatment


title: shScr3-11d


title: BrdU-Seq 19h

status: Public on Feb 17 2021

city: Birmingham

first: Marco

last: Saponaro

address: Vincent Drive

department: Institute of Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

library_source: genomic

data_processing:
Library strategy: BrdU-Seq
Paired-end BrdU-Seq reads were aligned to the hg38 genome assembly using Bowtie 2 v.2.3.3.1 (Langmead et al., 2012).
BAM files were sorted and indexed using SAMtools v.1.4 (Li et al., 2009).
The reads that mapped to region DAC blacklisted for mappability by the ENCODE project were removed.
Coverage calcualtion was done using the function “quantify” in EaSeq, from the start to the end of the gene of all annotated genes
Genome_build: hg38
Supplementary_files_format_and_content: .txt, containing the quantifications over each gene as above described

molecule: genomic DNA

source_name: fibroblast cells

growth_protocol: Human immortalized fibroblasts (BJ-hTERT cells) were cultured in DMEM (Sigma-Aldrich) supplemented with 10 % FBS, 2 mM L-glutamine and penicillin/streptomycin in 5 % CO2 at 37°C.

extract_protocol:
PureLink Genomic DNA Mini Kit (Thermo Fisher Scientific)
Illumina's Nextera XT DNA Library Preparation Kit following manufacturer’s protocol

treatment_protocol: Cells fully confluent were seeded at 20 % confluence in 150 mm dishes, and grown overnight. Cells were synchronized in the G0/G1 phase in serum starvation medium (DMEM supplemented with 0.2 % FBS, 2mM L-glutamine and penicillin/streptomycin) in 5 % CO2 at 37°C for 26 h, and released into S-phase with regular DMEM for the indicated timepoints. 15.5 h after release, 100 ng/ml nocodazole (Sigma-Aldrich) was added to the later timepoint cell cultures (19 h, 22 h, 24 h, 28 h) to prevent cells from re-entering the cell cycle. For the triptolide treatment, cells were treated for 1 hour with the indicated concentration before being harvested at the 16h timepoint.

tag: strain

value: hTERT-immortalized fibroblasts

tag: tissue

value: skin; foreskin

tag: brdu antibody

value: Mouse monoclonal anti-BrdU, Sigma-Aldrich, Cat#B8434

value: full kinetic 1


title: shBRD93-11d

value: lentivirus with shBRD9


title: ULDM2_2

status: Public on Nov 04 2020

city: Houston

first: Sara

middle: Chloe

last: Di Rienzi

state: TX

address: 1 Baylor Plaza Room 743E

department: Molecular Virology and Microbiology

institute: Baylor College of Medicine

data_processing:
Basecalling was performed using CASAVA version 1.8. Reads were filtered as follows: reads containing adaptors were removed, reads with more than 10% N reads were removed,reads where > 50% of the bases have Qscore <= 5 were removed.
Reads were aligned to hg19 human genome using STAR v2.5, with mismatch=2
Reads were quantified using HTSeq v0.6.1, with -m union
Genome_build: Homo_sapiens_hg19
Supplementary_files_format_and_content: One tab-delimited text file with the read counts for each Sample by each gene mapped

molecule: polyA RNA

source_name: uninduced NGN3 J2 human enteroids

growth_protocol: NGN3 J2 enteroids were propagated in 3D CMGF+ media + 10 umol Y-27632 Rock inhibitor + 200 ug/ml geneticin. NGN3 J2 enteroids were then seeded onto 24-well transwells and differentiated in the presence of differentiation media with or without 1 ug/ml doxycycline.

extract_protocol:
Transwell inserts were excised and placed in Trizol. Following a chloroform extraction, the aqueous phase was extracted using the Qiagen Rneasy Isolation Kit.
Paired-end Illumina sequencing libraries were prepared by Novogene. Briefly, total RNA was enriched for Eukaryote mRNA. mRNA was fragmented and cDNA synthesis proceeded using the standard NEB library construction.

treatment_protocol: All treatments were performed in differentiation media. LDM4 media was lyophilized and resuspended in differentiation media for use on the enteroids. LDM4 media recipe is provided in PMID 19210794.

value: human J2 (jejunal) enteroids

tag: induction

value: uninduced

tag: enteroid batch

tag: replicate


title: ILDM2_1

source_name: induced NGN3 J2 human enteroids

value: induced


title: BrdU-Seq 16h


title: shBRD92-11d


title: shBRD91-11d


title: ILDM2_3


title: BrdU-Seq 2 24h

value: full kinetic 2


title: Cd200+ Cardiac Fibroblasts 2 Chromatin Accessibility

status: Public on Sep 29 2020

city: New York

first: Silvia

middle: C

last: Hernandez

state: New York

address: 1300 Morris park avenue

department: Medicine- Cardiology

institute: Albert Einstein College of Medicine

description:
Cd200 Positive 2
Chromatin

data_processing:
ATAC-seq libraries were demultiplexed using Illumina bcl2fastq software.
Fastq files were aligned to the mouse (mm10) genome using bowtie2 (2.3.1) with the parameters --no-discordant, --no-mixed, --very-sensitive and -X 1000. The generated SAM files were sorted and converted to BAM files using samtools.
The generated SAM files were sorted and converted to BAM files using samtools.
Peak calling was done using MACS2 (2.1.0) with the parameters -q 0.5, -B, --call-summit and --keep-dup=all. Detected peaks were annotated to the UCSC mm10 known gene database (3.4.4) using ChIPpeakAnno R package.
Peak quantification was done using featureCounts implemented in Rsubread. Data transformation, normalization and testing for differential open chromatin regions were performed with DESeq2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: BigWig files with peak quantification.

organism: Mus musculus

source_name: heart

growth_protocol: Primary cell isolates from reporter mice.

extract_protocol:
Mouse cardiac interstitial cells (CIC) from healthy or infarcted 8-10 week old mice heart were obtained by enzymatic digestion. Erythrocytes were removed using RBC lysis buffer. A positive selection of CIC, enriched in Cardiac fibroblasts, was performed using LS columns and Feeder Removal MicroBeads (Miltenyi) according to the manufacturer’s instructions. GFP+/CD31-/CD45-, GFP+/CD200+/CD146- and GFP+/CD200-/CD146- cardiac fibroblasts (CF) were FACS-sorted in 1X PBS, 0.05% BSA.
Accessible chromatin mapping was performed using FAST-ATAC-seq with minor modifications. Cells were pelleted by centrifugation, then tagmented with 1 µL of TDE1 (Illumina) in 1X TD buffer , 0.042% digitonin (Promega) for 30 min at 37 °C and 450 rpm. Reactions were stopped at 4 °C for 5 min. Tagmented DNA molecules were released by incubation for 30 min at 40 °C with 5 µL of clean up buffer (900 mM NaCl (Sigma), 30 mM EDTA (Millipore)), 2 µL of 5% SDS (Millipore) and 2 µL of Proteinase K (NEB). PCR amplification allowed double barcoding of the samples, as well as addition of Illumina adaptors. Libraries were quantified using a Qubit 3.0 Fluorometer and their size profiles examined in Agilent’s 4200 TapeStation System.

tag: condition

value: 7dpi Cd200+

value: Cardiac Fibroblasts

tag: sorting strategy


title: 14dpi Cardiac Fibroblasts 1 Chromatin Accessibility

description:
14dpi 1
Chromatin


title: ILDM2_2


title: 7dpi Cardiac Fibroblasts 2 Chromatin Accessibility

description:
7dpi 2
Chromatin


title: Healthy Cardiac Fibroblasts 2 Chromatin Accessibility

description:
Healthy 2
Chromatin

value: Healthy


title: ILDM1_3


title: ILDM1_1


title: ULDM2_3


title: Cd200+ Cardiac Fibroblasts 1 Chromatin Accessibility

description:
Cd200 Positive 1
Chromatin


title: ULDM2_1


title: Col1a1 GFP+ Cardiac Fibroblasts 7 days post-infarction

description:
Single cell 3' RNA-seq
PolyA RNA
10X Barcode G2

data_processing:
Demultiplexing, alignment to the mouse (mm10) genome and quantification were performed using 10X Genomics Cell Ranger (v2.0).
Further analysis steps (quality control filtering, normalization, clustering and differential expression) were performed using R package Seurat (v2.3.4).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_FilteredGeneBCMatrices.h5: HDF5 Feature Barcode Matrix. Gene x Cells UMI count matrix.

source_name: Cardiac Fibroblasts

extract_protocol:
Mouse cardiac interstitial cells (CIC) from healthy or infarcted (7, 14 or 30 days post-infarction) 8-10 week old mice heart were obtained by enzymatic digestion. Erythrocytes were removed using RBC lysis buffer. A positive selection of CIC, enriched in Cardiac fibroblasts, was performed using LS columns and Feeder Removal MicroBeads (Miltenyi) according to the manufacturer's instructions. For Col1a1-GFP+ reporter mouse, GFP+/CD31-/CD45- cardiac fibroblasts (CF) were FACS-sorted in 1X PBS, 0.05% BSA. For Cthrc1-KO CIC cells, mEFSK4+/CD31-/CD45- cardiac fibroblasts (CF) were FACS-sorted in 1X PBS, 0.05% BSA.
Libraries were prepared using Single Cell 3’ Reagent Kits v2 (10X Genomics) according to the manufacturer’s instructions. Briefly, 16,000 cells were loaded at a concentration of 1,000 cells/µL on a Chromium Controller instrument (10X Genomics) to generate single-cell gel bead-in-emulsions (GEMs). Illumina adaptor sequences were added and the resulting library was amplified via end repair, A-tailing, adaptor ligation and PCR. Library quality control and quantification were performed using Qubit 3.0 Fluorometer (Life Technologies) and Agilent’s 4200 TapeStation System, respectively.

tag: strain/background

value: 7 days post infarction

value: Col1a1-GFP+ cells


title: ULDM1_3


title: ULDM1_2


title: 5dpi Cardiomyocyte 3

description:
5dpi_Cardiomyocyte_3
3' RNA-seq
PolyA RNA
Cardiomyocytes from infarcted 8-10 week old mice heart were obtained by standard Langendorff retrograde perfusion. Cells were collected by centrifugation and the pellet was homogenized with TRIzol™ Reagent (ThermoFisher). RNA isolation was performed according to the manufacturer's instructions.
processed data file: MusMusculus_Counts.txt
5dpi_Cardiomyocyte_3.fastq.gz

data_processing:
bcl2fastq was used to demultiplex .bcl files and retrieve fastq files according to the sample barcodes.
Fastq files were aligned to the corresponding genome (mm10, GRCh38, Sscrofa 11.1) using STAR (v 2.6.1).
Gene level quantification was performed using Rsubread and ensembl transcriptomes (GRCm38.91, Sscrofa11.1.93, and GRCh38.92).
Normalization, processing and differential expression analyses were performed using DEseq2.
Genome_build: Mouse mm10 (GRCm38), Human GRCh38, Pig Sscrofa 11.1
Supplementary_files_format_and_content: *_Counts.txt: Files with raw counts after gene level quantification.

source_name: Cardiomyocytes

extract_protocol:
Mouse cardiac interstitial cells (CIC) were obtained by enzymatic digestion. Erythrocytes were removed using RBC lysis buffer. A positive selection of CIC, enriched in Cardiac fibroblasts, was performed using LS columns and Feeder Removal MicroBeads (Miltenyi) according to the manufacturer’s instructions.
Bulk RNA-seq was performed following MARS-seq adapted for bulk RNA-seq with minor modifications. Briefly, poly-A RNA was extracted with Dynabeads Oligo dT (Ambion) and reverse-transcribed with AffinityScript Multiple Temperature Reverse Transcriptase (Agilent) using poly-dT oligos (IDT) carrying a 7-bp index. Up to 8 samples with similar overall RNA content were pooled together and subjected to linear amplification via IVT using HiScribe T7 High Yield RNA Synthesis Kit (New England Biolabs (NEB)). The resulting antisense RNA was fragmented into 250-350 bps fragments with RNA Fragmentation Reagents (Ambion) and dephosphorylated with 1U FastAP (Thermo Scientific) for 15 min at 37 °C. Partial Illumina adaptor sequences were ligated with T4 RNA Ligase 1 (NEB) followed by a second reverse transcription. Full Illumina adaptor sequences and a secondary barcode were added during library amplification with KAPA HiFi DNA Polymerase (Kapa Biosystems). Libraries were quantified using a Qubit 3.0 Fluorometer and their size profiles examined in Agilent’s 4200 TapeStation System. For Col1a1-GFP+ reporter mouse GFP+/CD31-/CD45- cardiac fibroblasts (CF), GFP-/CD31+/CD45- endothelial cells and GFP-/CD31-/CD45+ bone marrow-derived cells were FACS-sorted in Lysis/Binding Buffer (Ambion).

value: Cardiomyocytes


title: ULDM1_1


title: 14dpi Cardiac Fibroblasts 2 Chromatin Accessibility

description:
14dpi 2
Chromatin


title: 5dpi Cardiomyocyte 2

description:
5dpi_Cardiomyocyte_2
3' RNA-seq
PolyA RNA
Cardiomyocytes from infarcted 8-10 week old mice heart were obtained by standard Langendorff retrograde perfusion. Cells were collected by centrifugation and the pellet was homogenized with TRIzol™ Reagent (ThermoFisher). RNA isolation was performed according to the manufacturer's instructions.
processed data file: MusMusculus_Counts.txt
5dpi_Cardiomyocyte_2.fastq.gz


title: 30dpi Cardiac Fibroblasts 2 Chromatin Accessibility

description:
30dpi 2
Chromatin


title: Cd200- Cardiac Fibroblasts 1 Chromatin Accessibility

description:
Cd200 Negative 1
Chromatin

value: 7dpi Cd200-


title: 5dpi Cardiomyocyte 1

description:
5dpi_Cardiomyocyte_1
3' RNA-seq
PolyA RNA
Cardiomyocytes from infarcted 8-10 week old mice heart were obtained by standard Langendorff retrograde perfusion. Cells were collected by centrifugation and the pellet was homogenized with TRIzol™ Reagent (ThermoFisher). RNA isolation was performed according to the manufacturer's instructions.
processed data file: MusMusculus_Counts.txt
5dpi_Cardiomyocyte_1.fastq.gz


title: ILDM1_2


title: 30dpi Cardiac Fibroblasts 1 Chromatin Accessibility

description:
30dpi 1
Chromatin


title: 5dpi WT CD31 Positive 2

description:
5dpi_WT_CD31_2
3' RNA-seq
PolyA RNA
For Cthrc1-KO and Cthrc1-WT CIC cells, mEFSK4+/CD31-/CD45- cardiac fibroblasts (CF), mEFSK4-/CD31+/CD45- endothelial cells and mEFSK4-/CD31-/CD45+ bone marrow-derived cells were FACS-sorted in Lysis/Binding Buffer (Ambion).
processed data file: MusMusculus_Counts.txt
5dpi_WT_CD31_2.fastq.gz

source_name: CD31+ cells

value: Endothelial

tag: other details

value: WT (for Cthrc1-KO strain)


title: 5dpi Cthrc1-KO mEFSK4 Positive 2

description:
5dpi_Cthrc1KO_mEFSK4_2
3' RNA-seq
PolyA RNA
For Cthrc1-KO and Cthrc1-WT CIC cells, mEFSK4+/CD31-/CD45- cardiac fibroblasts (CF), mEFSK4-/CD31+/CD45- endothelial cells and mEFSK4-/CD31-/CD45+ bone marrow-derived cells were FACS-sorted in Lysis/Binding Buffer (Ambion).
processed data file: MusMusculus_Counts.txt
5dpi_Cthrc1KO_mEFSK4_2.fastq.gz

value: 5dpi Cthrc1KO

value: mEFSK4+ Cardiac Fibroblasts


title: Healthy Cardiac Fibroblasts 1 Chromatin Accessibility

description:
Healthy 1
Chromatin


title: mEFSK4+ Cardiac Fibroblast from Cthrc1-KO mice 7 days after MI

description:
Single cell 3' RNA-seq
PolyA RNA
10X Barcode B3

value: Cthrc1-KO 7days post infarction

value: mEFSk4+ cells


title: 7dpi Cardiac Fibroblasts 1 Chromatin Accessibility

description:
7dpi 1
Chromatin


title: Cd200- Cardiac Fibroblasts 2 Chromatin Accessibility

description:
Cd200 Negative 2
Chromatin


title: 5dpi Cthrc1-KO CD45 Positive 2

description:
5dpi_Cthrc1KO_CD45_2
3' RNA-seq
PolyA RNA
For Cthrc1-KO and Cthrc1-WT CIC cells, mEFSK4+/CD31-/CD45- cardiac fibroblasts (CF), mEFSK4-/CD31+/CD45- endothelial cells and mEFSK4-/CD31-/CD45+ bone marrow-derived cells were FACS-sorted in Lysis/Binding Buffer (Ambion).
processed data file: MusMusculus_Counts.txt
5dpi_Cthrc1KO_CD45_2.fastq.gz

source_name: CD45+ cells

value: Bone Marrow-Derived


title: Col1a1 GFP+ Cardiac Fibroblasts from Healthy Myocardium

description:
Single cell 3' RNA-seq
PolyA RNA
10X Barcode D2

value: Healthy Myocardium


title: 5dpi Cthrc1-KO CD31 Positive 1

description:
5dpi_Cthrc1KO_CD31_1
3' RNA-seq
PolyA RNA
For Cthrc1-KO and Cthrc1-WT CIC cells, mEFSK4+/CD31-/CD45- cardiac fibroblasts (CF), mEFSK4-/CD31+/CD45- endothelial cells and mEFSK4-/CD31-/CD45+ bone marrow-derived cells were FACS-sorted in Lysis/Binding Buffer (Ambion).
processed data file: MusMusculus_Counts.txt
5dpi_Cthrc1KO_CD31_1.fastq.gz


title: TGFB + LY Cultivated Fibroblasts 3

description:
TGFB-LY_CultivatedFBs_3
3' RNA-seq
PolyA RNA
Primary mouse cardiac fibroblasts; Mouse cardiac interstitial cells (CIC) from healthy or infarcted 8-10 week old mice heart were obtained by enzymatic digestion. Erythrocytes were removed using RBC lysis buffer and CIC pellet was resuspended in complete medium (DMEM + 10% FBS + 1% P/S + 1% L-Glu) containing 10 ng/mL of bFGF. For TGF- β signalling pathways in vitro functional assays, after 24 hours in passage 2, cultured CF were incubated in starving conditions (complete DMEM without FBS) overnight, and then the medium was supplemented with hTGF-β1 (10 ng/mL), hTGF-β1 (10 ng/mL) and LY294002 (40 µM) or DMSO (used as vehicle) for 48 hours. Controls without supplement were included in the study. Treated CF were collected in Lysis/Binding Buffer.
processed data file: MusMusculus_Counts.txt
TGFB-LY_CultivatedFBs_3.fastq.gz

value: Cultivated

value: Cultivated Cardiac Fibroblasts

value: TGFB + PI3K/AKT Inhibitor


title: TGFB + LY Cultivated Fibroblasts 2

description:
TGFB-LY_CultivatedFBs_2
3' RNA-seq
PolyA RNA
Primary mouse cardiac fibroblasts; Mouse cardiac interstitial cells (CIC) from healthy or infarcted 8-10 week old mice heart were obtained by enzymatic digestion. Erythrocytes were removed using RBC lysis buffer and CIC pellet was resuspended in complete medium (DMEM + 10% FBS + 1% P/S + 1% L-Glu) containing 10 ng/mL of bFGF. For TGF- β signalling pathways in vitro functional assays, after 24 hours in passage 2, cultured CF were incubated in starving conditions (complete DMEM without FBS) overnight, and then the medium was supplemented with hTGF-β1 (10 ng/mL), hTGF-β1 (10 ng/mL) and LY294002 (40 µM) or DMSO (used as vehicle) for 48 hours. Controls without supplement were included in the study. Treated CF were collected in Lysis/Binding Buffer.
processed data file: MusMusculus_Counts.txt
TGFB-LY_CultivatedFBs_2.fastq.gz


title: 5dpi WT CD45 Positive 2

description:
5dpi_WT_CD45_2
3' RNA-seq
PolyA RNA
For Cthrc1-KO and Cthrc1-WT CIC cells, mEFSK4+/CD31-/CD45- cardiac fibroblasts (CF), mEFSK4-/CD31+/CD45- endothelial cells and mEFSK4-/CD31-/CD45+ bone marrow-derived cells were FACS-sorted in Lysis/Binding Buffer (Ambion).
processed data file: MusMusculus_Counts.txt
5dpi_WT_CD45_2.fastq.gz


title: 5dpi WT mEFSK4 Positive 2

description:
5dpi_WT_mEFSK4_2
3' RNA-seq
PolyA RNA
For Cthrc1-KO and Cthrc1-WT CIC cells, mEFSK4+/CD31-/CD45- cardiac fibroblasts (CF), mEFSK4-/CD31+/CD45- endothelial cells and mEFSK4-/CD31-/CD45+ bone marrow-derived cells were FACS-sorted in Lysis/Binding Buffer (Ambion).
processed data file: MusMusculus_Counts.txt
5dpi_WT_mEFSK4_2.fastq.gz


title: TGFB + DMSO Cultivated Fibroblasts 2

description:
TGFB-DMSO_CultivatedFBs_2
3' RNA-seq
PolyA RNA
Primary mouse cardiac fibroblasts; Mouse cardiac interstitial cells (CIC) from healthy or infarcted 8-10 week old mice heart were obtained by enzymatic digestion. Erythrocytes were removed using RBC lysis buffer and CIC pellet was resuspended in complete medium (DMEM + 10% FBS + 1% P/S + 1% L-Glu) containing 10 ng/mL of bFGF. For TGF- β signalling pathways in vitro functional assays, after 24 hours in passage 2, cultured CF were incubated in starving conditions (complete DMEM without FBS) overnight, and then the medium was supplemented with hTGF-β1 (10 ng/mL), hTGF-β1 (10 ng/mL) and LY294002 (40 µM) or DMSO (used as vehicle) for 48 hours. Controls without supplement were included in the study. Treated CF were collected in Lysis/Binding Buffer.
processed data file: MusMusculus_Counts.txt
TGFB-DMSO_CultivatedFBs_2.fastq.gz

value: TGFB + vehicle


title: 5dpi WT CD45 Positive 1

description:
5dpi_WT_CD45_1
3' RNA-seq
PolyA RNA
For Cthrc1-KO and Cthrc1-WT CIC cells, mEFSK4+/CD31-/CD45- cardiac fibroblasts (CF), mEFSK4-/CD31+/CD45- endothelial cells and mEFSK4-/CD31-/CD45+ bone marrow-derived cells were FACS-sorted in Lysis/Binding Buffer (Ambion).
processed data file: MusMusculus_Counts.txt
5dpi_WT_CD45_1.fastq.gz


title: 5dpi WT CD31 Positive 1

description:
5dpi_WT_CD31_1
3' RNA-seq
PolyA RNA
For Cthrc1-KO and Cthrc1-WT CIC cells, mEFSK4+/CD31-/CD45- cardiac fibroblasts (CF), mEFSK4-/CD31+/CD45- endothelial cells and mEFSK4-/CD31-/CD45+ bone marrow-derived cells were FACS-sorted in Lysis/Binding Buffer (Ambion).
processed data file: MusMusculus_Counts.txt
5dpi_WT_CD31_1.fastq.gz


title: TGFB + LY Cultivated Fibroblasts 4

description:
TGFB-LY_CultivatedFBs_4
3' RNA-seq
PolyA RNA
Primary mouse cardiac fibroblasts; Mouse cardiac interstitial cells (CIC) from healthy or infarcted 8-10 week old mice heart were obtained by enzymatic digestion. Erythrocytes were removed using RBC lysis buffer and CIC pellet was resuspended in complete medium (DMEM + 10% FBS + 1% P/S + 1% L-Glu) containing 10 ng/mL of bFGF. For TGF- β signalling pathways in vitro functional assays, after 24 hours in passage 2, cultured CF were incubated in starving conditions (complete DMEM without FBS) overnight, and then the medium was supplemented with hTGF-β1 (10 ng/mL), hTGF-β1 (10 ng/mL) and LY294002 (40 µM) or DMSO (used as vehicle) for 48 hours. Controls without supplement were included in the study. Treated CF were collected in Lysis/Binding Buffer.
processed data file: MusMusculus_Counts.txt
TGFB-LY_CultivatedFBs_4.fastq.gz


title: Col1a1 GFP+ Cardiac Fibroblasts 30 days post-infarction

description:
Single cell 3' RNA-seq
PolyA RNA
10X Barcode A3

value: 30 days post infarction


title: TGFB + DMSO Cultivated Fibroblasts 4

description:
TGFB-DMSO_CultivatedFBs_4
3' RNA-seq
PolyA RNA
Primary mouse cardiac fibroblasts; Mouse cardiac interstitial cells (CIC) from healthy or infarcted 8-10 week old mice heart were obtained by enzymatic digestion. Erythrocytes were removed using RBC lysis buffer and CIC pellet was resuspended in complete medium (DMEM + 10% FBS + 1% P/S + 1% L-Glu) containing 10 ng/mL of bFGF. For TGF- β signalling pathways in vitro functional assays, after 24 hours in passage 2, cultured CF were incubated in starving conditions (complete DMEM without FBS) overnight, and then the medium was supplemented with hTGF-β1 (10 ng/mL), hTGF-β1 (10 ng/mL) and LY294002 (40 µM) or DMSO (used as vehicle) for 48 hours. Controls without supplement were included in the study. Treated CF were collected in Lysis/Binding Buffer.
processed data file: MusMusculus_Counts.txt
TGFB-DMSO_CultivatedFBs_4.fastq.gz


title: 5dpi WT mEFSK4 Positive 1

description:
5dpi_WT_mEFSK4_1
3' RNA-seq
PolyA RNA
For Cthrc1-KO and Cthrc1-WT CIC cells, mEFSK4+/CD31-/CD45- cardiac fibroblasts (CF), mEFSK4-/CD31+/CD45- endothelial cells and mEFSK4-/CD31-/CD45+ bone marrow-derived cells were FACS-sorted in Lysis/Binding Buffer (Ambion).
processed data file: MusMusculus_Counts.txt
5dpi_WT_mEFSK4_1.fastq.gz


title: TGFB Cultivated Fibroblasts 4

description:
TGFB_CultivatedFBs_4
3' RNA-seq
PolyA RNA
Primary mouse cardiac fibroblasts; Mouse cardiac interstitial cells (CIC) from healthy or infarcted 8-10 week old mice heart were obtained by enzymatic digestion. Erythrocytes were removed using RBC lysis buffer and CIC pellet was resuspended in complete medium (DMEM + 10% FBS + 1% P/S + 1% L-Glu) containing 10 ng/mL of bFGF. For TGF- β signalling pathways in vitro functional assays, after 24 hours in passage 2, cultured CF were incubated in starving conditions (complete DMEM without FBS) overnight, and then the medium was supplemented with hTGF-β1 (10 ng/mL), hTGF-β1 (10 ng/mL) and LY294002 (40 µM) or DMSO (used as vehicle) for 48 hours. Controls without supplement were included in the study. Treated CF were collected in Lysis/Binding Buffer.
processed data file: MusMusculus_Counts.txt
TGFB_CultivatedFBs_4.fastq.gz

value: TGFB


title: Col1a1 GFP+ Cardiac Fibroblasts 14 days post-infarction

description:
Single cell 3' RNA-seq
PolyA RNA
10X Barcode C3

value: 14 days post infarction

value: Col1a1-GFP+ cells


title: TGFB Cultivated Fibroblasts 3

description:
TGFB_CultivatedFBs_3
3' RNA-seq
PolyA RNA
Primary mouse cardiac fibroblasts; Mouse cardiac interstitial cells (CIC) from healthy or infarcted 8-10 week old mice heart were obtained by enzymatic digestion. Erythrocytes were removed using RBC lysis buffer and CIC pellet was resuspended in complete medium (DMEM + 10% FBS + 1% P/S + 1% L-Glu) containing 10 ng/mL of bFGF. For TGF- β signalling pathways in vitro functional assays, after 24 hours in passage 2, cultured CF were incubated in starving conditions (complete DMEM without FBS) overnight, and then the medium was supplemented with hTGF-β1 (10 ng/mL), hTGF-β1 (10 ng/mL) and LY294002 (40 µM) or DMSO (used as vehicle) for 48 hours. Controls without supplement were included in the study. Treated CF were collected in Lysis/Binding Buffer.
processed data file: MusMusculus_Counts.txt
TGFB_CultivatedFBs_3.fastq.gz


title: 5dpi Cthrc1-KO mEFSK4 Positive 1

description:
5dpi_Cthrc1KO_mEFSK4_1
3' RNA-seq
PolyA RNA
For Cthrc1-KO and Cthrc1-WT CIC cells, mEFSK4+/CD31-/CD45- cardiac fibroblasts (CF), mEFSK4-/CD31+/CD45- endothelial cells and mEFSK4-/CD31-/CD45+ bone marrow-derived cells were FACS-sorted in Lysis/Binding Buffer (Ambion).
processed data file: MusMusculus_Counts.txt
5dpi_Cthrc1KO_mEFSK4_1.fastq.gz


title: Control TGFB Cultivated Fibroblasts 4

description:
Control_CultivatedFBs_4
3' RNA-seq
PolyA RNA
Primary mouse cardiac fibroblasts; Mouse cardiac interstitial cells (CIC) from healthy or infarcted 8-10 week old mice heart were obtained by enzymatic digestion. Erythrocytes were removed using RBC lysis buffer and CIC pellet was resuspended in complete medium (DMEM + 10% FBS + 1% P/S + 1% L-Glu) containing 10 ng/mL of bFGF. For TGF- β signalling pathways in vitro functional assays, after 24 hours in passage 2, cultured CF were incubated in starving conditions (complete DMEM without FBS) overnight, and then the medium was supplemented with hTGF-β1 (10 ng/mL), hTGF-β1 (10 ng/mL) and LY294002 (40 µM) or DMSO (used as vehicle) for 48 hours. Controls without supplement were included in the study. Treated CF were collected in Lysis/Binding Buffer.
processed data file: MusMusculus_Counts.txt
Control_CultivatedFBs_4.fastq.gz

value: Control for TGFB


title: 5dpi Cthrc1-KO CD45 Positive 1

description:
5dpi_Cthrc1KO_CD45_1
3' RNA-seq
PolyA RNA
For Cthrc1-KO and Cthrc1-WT CIC cells, mEFSK4+/CD31-/CD45- cardiac fibroblasts (CF), mEFSK4-/CD31+/CD45- endothelial cells and mEFSK4-/CD31-/CD45+ bone marrow-derived cells were FACS-sorted in Lysis/Binding Buffer (Ambion).
processed data file: MusMusculus_Counts.txt
5dpi_Cthrc1KO_CD45_1.fastq.gz


title: Control TGFB Cultivated Fibroblasts 1

description:
Control_CultivatedFBs_1
3' RNA-seq
PolyA RNA
Primary mouse cardiac fibroblasts; Mouse cardiac interstitial cells (CIC) from healthy or infarcted 8-10 week old mice heart were obtained by enzymatic digestion. Erythrocytes were removed using RBC lysis buffer and CIC pellet was resuspended in complete medium (DMEM + 10% FBS + 1% P/S + 1% L-Glu) containing 10 ng/mL of bFGF. For TGF- β signalling pathways in vitro functional assays, after 24 hours in passage 2, cultured CF were incubated in starving conditions (complete DMEM without FBS) overnight, and then the medium was supplemented with hTGF-β1 (10 ng/mL), hTGF-β1 (10 ng/mL) and LY294002 (40 µM) or DMSO (used as vehicle) for 48 hours. Controls without supplement were included in the study. Treated CF were collected in Lysis/Binding Buffer.
processed data file: MusMusculus_Counts.txt
Control_CultivatedFBs_1.fastq.gz


title: 5dpi Cthrc1-KO CD31 Positive 2

description:
5dpi_Cthrc1KO_CD31_2
3' RNA-seq
PolyA RNA
For Cthrc1-KO and Cthrc1-WT CIC cells, mEFSK4+/CD31-/CD45- cardiac fibroblasts (CF), mEFSK4-/CD31+/CD45- endothelial cells and mEFSK4-/CD31-/CD45+ bone marrow-derived cells were FACS-sorted in Lysis/Binding Buffer (Ambion).
processed data file: MusMusculus_Counts.txt
5dpi_Cthrc1KO_CD31_2.fastq.gz

value: Endothelial


title: Sox9 LV Cultivated Fibroblasts 6

description:
Sox9_CultivatedFBs_LV_6
3' RNA-seq
PolyA RNA
Primary mouse cardiac fibroblasts; Mouse cardiac interstitial cells (CIC) from healthy or infarcted 8-10 week old mice heart were obtained by enzymatic digestion. Erythrocytes were removed using RBC lysis buffer and CIC pellet was resuspended in complete medium (DMEM + 10% FBS + 1% P/S + 1% L-Glu) containing 10 ng/mL of bFGF. For Transcription factors in vitro functional assays, lentiviral transduction was performed in passage 1 CF in cultured medium supplemented with 8 µg/mL polybrene. After addition of the virus, cell plates were centrifuged at 2,000 rpm for 90 min at 32 °C two consecutive days. The cells were incubated for 72 hours from the first infection, they were subculture from passage 1 to 2. After four days in culture (passage 2) cells were trypsinized and sorted in 100 µL of Lysis/Binding Buffer, vortexed and stored at -80 °C until further processing.
processed data file: MusMusculus_Counts.txt
Sox9_CultivatedFBs_LV_6.fastq.gz

value: Sox9 Lentivirus


title: Sox9 LV Cultivated Fibroblasts 5

description:
Sox9_CultivatedFBs_LV_5
3' RNA-seq
PolyA RNA
Primary mouse cardiac fibroblasts; Mouse cardiac interstitial cells (CIC) from healthy or infarcted 8-10 week old mice heart were obtained by enzymatic digestion. Erythrocytes were removed using RBC lysis buffer and CIC pellet was resuspended in complete medium (DMEM + 10% FBS + 1% P/S + 1% L-Glu) containing 10 ng/mL of bFGF. For Transcription factors in vitro functional assays, lentiviral transduction was performed in passage 1 CF in cultured medium supplemented with 8 µg/mL polybrene. After addition of the virus, cell plates were centrifuged at 2,000 rpm for 90 min at 32 °C two consecutive days. The cells were incubated for 72 hours from the first infection, they were subculture from passage 1 to 2. After four days in culture (passage 2) cells were trypsinized and sorted in 100 µL of Lysis/Binding Buffer, vortexed and stored at -80 °C until further processing.
processed data file: MusMusculus_Counts.txt
Sox9_CultivatedFBs_LV_5.fastq.gz


title: TGFB + LY Cultivated Fibroblasts 1

description:
TGFB-LY_CultivatedFBs_1
3' RNA-seq
PolyA RNA
Primary mouse cardiac fibroblasts; Mouse cardiac interstitial cells (CIC) from healthy or infarcted 8-10 week old mice heart were obtained by enzymatic digestion. Erythrocytes were removed using RBC lysis buffer and CIC pellet was resuspended in complete medium (DMEM + 10% FBS + 1% P/S + 1% L-Glu) containing 10 ng/mL of bFGF. For TGF- β signalling pathways in vitro functional assays, after 24 hours in passage 2, cultured CF were incubated in starving conditions (complete DMEM without FBS) overnight, and then the medium was supplemented with hTGF-β1 (10 ng/mL), hTGF-β1 (10 ng/mL) and LY294002 (40 µM) or DMSO (used as vehicle) for 48 hours. Controls without supplement were included in the study. Treated CF were collected in Lysis/Binding Buffer.
processed data file: MusMusculus_Counts.txt
TGFB-LY_CultivatedFBs_1.fastq.gz


title: TGFB + DMSO Cultivated Fibroblasts 3

description:
TGFB-DMSO_CultivatedFBs_3
3' RNA-seq
PolyA RNA
Primary mouse cardiac fibroblasts; Mouse cardiac interstitial cells (CIC) from healthy or infarcted 8-10 week old mice heart were obtained by enzymatic digestion. Erythrocytes were removed using RBC lysis buffer and CIC pellet was resuspended in complete medium (DMEM + 10% FBS + 1% P/S + 1% L-Glu) containing 10 ng/mL of bFGF. For TGF- β signalling pathways in vitro functional assays, after 24 hours in passage 2, cultured CF were incubated in starving conditions (complete DMEM without FBS) overnight, and then the medium was supplemented with hTGF-β1 (10 ng/mL), hTGF-β1 (10 ng/mL) and LY294002 (40 µM) or DMSO (used as vehicle) for 48 hours. Controls without supplement were included in the study. Treated CF were collected in Lysis/Binding Buffer.
processed data file: MusMusculus_Counts.txt
TGFB-DMSO_CultivatedFBs_3.fastq.gz


title: Sox9 LV Cultivated Fibroblasts 2

description:
Sox9_CultivatedFBs_LV_2
3' RNA-seq
PolyA RNA
Primary mouse cardiac fibroblasts; Mouse cardiac interstitial cells (CIC) from healthy or infarcted 8-10 week old mice heart were obtained by enzymatic digestion. Erythrocytes were removed using RBC lysis buffer and CIC pellet was resuspended in complete medium (DMEM + 10% FBS + 1% P/S + 1% L-Glu) containing 10 ng/mL of bFGF. For Transcription factors in vitro functional assays, lentiviral transduction was performed in passage 1 CF in cultured medium supplemented with 8 µg/mL polybrene. After addition of the virus, cell plates were centrifuged at 2,000 rpm for 90 min at 32 °C two consecutive days. The cells were incubated for 72 hours from the first infection, they were subculture from passage 1 to 2. After four days in culture (passage 2) cells were trypsinized and sorted in 100 µL of Lysis/Binding Buffer, vortexed and stored at -80 °C until further processing.
processed data file: MusMusculus_Counts.txt
Sox9_CultivatedFBs_LV_2.fastq.gz


title: TGFB + DMSO Cultivated Fibroblasts 1

description:
TGFB-DMSO_CultivatedFBs_1
3' RNA-seq
PolyA RNA
Primary mouse cardiac fibroblasts; Mouse cardiac interstitial cells (CIC) from healthy or infarcted 8-10 week old mice heart were obtained by enzymatic digestion. Erythrocytes were removed using RBC lysis buffer and CIC pellet was resuspended in complete medium (DMEM + 10% FBS + 1% P/S + 1% L-Glu) containing 10 ng/mL of bFGF. For TGF- β signalling pathways in vitro functional assays, after 24 hours in passage 2, cultured CF were incubated in starving conditions (complete DMEM without FBS) overnight, and then the medium was supplemented with hTGF-β1 (10 ng/mL), hTGF-β1 (10 ng/mL) and LY294002 (40 µM) or DMSO (used as vehicle) for 48 hours. Controls without supplement were included in the study. Treated CF were collected in Lysis/Binding Buffer.
processed data file: MusMusculus_Counts.txt
TGFB-DMSO_CultivatedFBs_1.fastq.gz


title: Runx1 LV Cultivated Fibroblasts 6

description:
Runx1_CultivatedFBs_LV_6
3' RNA-seq
PolyA RNA
Primary mouse cardiac fibroblasts; Mouse cardiac interstitial cells (CIC) from healthy or infarcted 8-10 week old mice heart were obtained by enzymatic digestion. Erythrocytes were removed using RBC lysis buffer and CIC pellet was resuspended in complete medium (DMEM + 10% FBS + 1% P/S + 1% L-Glu) containing 10 ng/mL of bFGF. For Transcription factors in vitro functional assays, lentiviral transduction was performed in passage 1 CF in cultured medium supplemented with 8 µg/mL polybrene. After addition of the virus, cell plates were centrifuged at 2,000 rpm for 90 min at 32 °C two consecutive days. The cells were incubated for 72 hours from the first infection, they were subculture from passage 1 to 2. After four days in culture (passage 2) cells were trypsinized and sorted in 100 µL of Lysis/Binding Buffer, vortexed and stored at -80 °C until further processing.
processed data file: MusMusculus_Counts.txt
Runx1_CultivatedFBs_LV_6.fastq.gz

value: Runx1 Lentivirus


title: Sox9 LV Cultivated Fibroblasts 1

description:
Sox9_CultivatedFBs_LV_1
3' RNA-seq
PolyA RNA
Primary mouse cardiac fibroblasts; Mouse cardiac interstitial cells (CIC) from healthy or infarcted 8-10 week old mice heart were obtained by enzymatic digestion. Erythrocytes were removed using RBC lysis buffer and CIC pellet was resuspended in complete medium (DMEM + 10% FBS + 1% P/S + 1% L-Glu) containing 10 ng/mL of bFGF. For Transcription factors in vitro functional assays, lentiviral transduction was performed in passage 1 CF in cultured medium supplemented with 8 µg/mL polybrene. After addition of the virus, cell plates were centrifuged at 2,000 rpm for 90 min at 32 °C two consecutive days. The cells were incubated for 72 hours from the first infection, they were subculture from passage 1 to 2. After four days in culture (passage 2) cells were trypsinized and sorted in 100 µL of Lysis/Binding Buffer, vortexed and stored at -80 °C until further processing.
processed data file: MusMusculus_Counts.txt
Sox9_CultivatedFBs_LV_1.fastq.gz


title: TGFB Cultivated Fibroblasts 2

description:
TGFB_CultivatedFBs_2
3' RNA-seq
PolyA RNA
Primary mouse cardiac fibroblasts; Mouse cardiac interstitial cells (CIC) from healthy or infarcted 8-10 week old mice heart were obtained by enzymatic digestion. Erythrocytes were removed using RBC lysis buffer and CIC pellet was resuspended in complete medium (DMEM + 10% FBS + 1% P/S + 1% L-Glu) containing 10 ng/mL of bFGF. For TGF- β signalling pathways in vitro functional assays, after 24 hours in passage 2, cultured CF were incubated in starving conditions (complete DMEM without FBS) overnight, and then the medium was supplemented with hTGF-β1 (10 ng/mL), hTGF-β1 (10 ng/mL) and LY294002 (40 µM) or DMSO (used as vehicle) for 48 hours. Controls without supplement were included in the study. Treated CF were collected in Lysis/Binding Buffer.
processed data file: MusMusculus_Counts.txt
TGFB_CultivatedFBs_2.fastq.gz


title: Runx1 LV Cultivated Fibroblasts 4

description:
Runx1_CultivatedFBs_LV_4
3' RNA-seq
PolyA RNA
Primary mouse cardiac fibroblasts; Mouse cardiac interstitial cells (CIC) from healthy or infarcted 8-10 week old mice heart were obtained by enzymatic digestion. Erythrocytes were removed using RBC lysis buffer and CIC pellet was resuspended in complete medium (DMEM + 10% FBS + 1% P/S + 1% L-Glu) containing 10 ng/mL of bFGF. For Transcription factors in vitro functional assays, lentiviral transduction was performed in passage 1 CF in cultured medium supplemented with 8 µg/mL polybrene. After addition of the virus, cell plates were centrifuged at 2,000 rpm for 90 min at 32 °C two consecutive days. The cells were incubated for 72 hours from the first infection, they were subculture from passage 1 to 2. After four days in culture (passage 2) cells were trypsinized and sorted in 100 µL of Lysis/Binding Buffer, vortexed and stored at -80 °C until further processing.
processed data file: MusMusculus_Counts.txt
Runx1_CultivatedFBs_LV_4.fastq.gz


title: Runx1 LV Cultivated Fibroblasts 2

description:
Runx1_CultivatedFBs_LV_2
3' RNA-seq
PolyA RNA
Primary mouse cardiac fibroblasts; Mouse cardiac interstitial cells (CIC) from healthy or infarcted 8-10 week old mice heart were obtained by enzymatic digestion. Erythrocytes were removed using RBC lysis buffer and CIC pellet was resuspended in complete medium (DMEM + 10% FBS + 1% P/S + 1% L-Glu) containing 10 ng/mL of bFGF. For Transcription factors in vitro functional assays, lentiviral transduction was performed in passage 1 CF in cultured medium supplemented with 8 µg/mL polybrene. After addition of the virus, cell plates were centrifuged at 2,000 rpm for 90 min at 32 °C two consecutive days. The cells were incubated for 72 hours from the first infection, they were subculture from passage 1 to 2. After four days in culture (passage 2) cells were trypsinized and sorted in 100 µL of Lysis/Binding Buffer, vortexed and stored at -80 °C until further processing.
processed data file: MusMusculus_Counts.txt
Runx1_CultivatedFBs_LV_2.fastq.gz


title: TGFB Cultivated Fibroblasts 1

description:
TGFB_CultivatedFBs_1
3' RNA-seq
PolyA RNA
Primary mouse cardiac fibroblasts; Mouse cardiac interstitial cells (CIC) from healthy or infarcted 8-10 week old mice heart were obtained by enzymatic digestion. Erythrocytes were removed using RBC lysis buffer and CIC pellet was resuspended in complete medium (DMEM + 10% FBS + 1% P/S + 1% L-Glu) containing 10 ng/mL of bFGF. For TGF- β signalling pathways in vitro functional assays, after 24 hours in passage 2, cultured CF were incubated in starving conditions (complete DMEM without FBS) overnight, and then the medium was supplemented with hTGF-β1 (10 ng/mL), hTGF-β1 (10 ng/mL) and LY294002 (40 µM) or DMSO (used as vehicle) for 48 hours. Controls without supplement were included in the study. Treated CF were collected in Lysis/Binding Buffer.
processed data file: MusMusculus_Counts.txt
TGFB_CultivatedFBs_1.fastq.gz


title: Control TGFB Cultivated Fibroblasts 3

description:
Control_CultivatedFBs_3
3' RNA-seq
PolyA RNA
Primary mouse cardiac fibroblasts; Mouse cardiac interstitial cells (CIC) from healthy or infarcted 8-10 week old mice heart were obtained by enzymatic digestion. Erythrocytes were removed using RBC lysis buffer and CIC pellet was resuspended in complete medium (DMEM + 10% FBS + 1% P/S + 1% L-Glu) containing 10 ng/mL of bFGF. For TGF- β signalling pathways in vitro functional assays, after 24 hours in passage 2, cultured CF were incubated in starving conditions (complete DMEM without FBS) overnight, and then the medium was supplemented with hTGF-β1 (10 ng/mL), hTGF-β1 (10 ng/mL) and LY294002 (40 µM) or DMSO (used as vehicle) for 48 hours. Controls without supplement were included in the study. Treated CF were collected in Lysis/Binding Buffer.
processed data file: MusMusculus_Counts.txt
Control_CultivatedFBs_3.fastq.gz


title: Control TGFB Cultivated Fibroblasts 2

description:
Control_CultivatedFBs_2
3' RNA-seq
PolyA RNA
Primary mouse cardiac fibroblasts; Mouse cardiac interstitial cells (CIC) from healthy or infarcted 8-10 week old mice heart were obtained by enzymatic digestion. Erythrocytes were removed using RBC lysis buffer and CIC pellet was resuspended in complete medium (DMEM + 10% FBS + 1% P/S + 1% L-Glu) containing 10 ng/mL of bFGF. For TGF- β signalling pathways in vitro functional assays, after 24 hours in passage 2, cultured CF were incubated in starving conditions (complete DMEM without FBS) overnight, and then the medium was supplemented with hTGF-β1 (10 ng/mL), hTGF-β1 (10 ng/mL) and LY294002 (40 µM) or DMSO (used as vehicle) for 48 hours. Controls without supplement were included in the study. Treated CF were collected in Lysis/Binding Buffer.
processed data file: MusMusculus_Counts.txt
Control_CultivatedFBs_2.fastq.gz


title: Sox9 LV Cultivated Fibroblasts 3

description:
Sox9_CultivatedFBs_LV_3
3' RNA-seq
PolyA RNA
Primary mouse cardiac fibroblasts; Mouse cardiac interstitial cells (CIC) from healthy or infarcted 8-10 week old mice heart were obtained by enzymatic digestion. Erythrocytes were removed using RBC lysis buffer and CIC pellet was resuspended in complete medium (DMEM + 10% FBS + 1% P/S + 1% L-Glu) containing 10 ng/mL of bFGF. For Transcription factors in vitro functional assays, lentiviral transduction was performed in passage 1 CF in cultured medium supplemented with 8 µg/mL polybrene. After addition of the virus, cell plates were centrifuged at 2,000 rpm for 90 min at 32 °C two consecutive days. The cells were incubated for 72 hours from the first infection, they were subculture from passage 1 to 2. After four days in culture (passage 2) cells were trypsinized and sorted in 100 µL of Lysis/Binding Buffer, vortexed and stored at -80 °C until further processing.
processed data file: MusMusculus_Counts.txt
Sox9_CultivatedFBs_LV_3.fastq.gz


title: Sox9 LV Cultivated Fibroblasts 4

description:
Sox9_CultivatedFBs_LV_4
3' RNA-seq
PolyA RNA
Primary mouse cardiac fibroblasts; Mouse cardiac interstitial cells (CIC) from healthy or infarcted 8-10 week old mice heart were obtained by enzymatic digestion. Erythrocytes were removed using RBC lysis buffer and CIC pellet was resuspended in complete medium (DMEM + 10% FBS + 1% P/S + 1% L-Glu) containing 10 ng/mL of bFGF. For Transcription factors in vitro functional assays, lentiviral transduction was performed in passage 1 CF in cultured medium supplemented with 8 µg/mL polybrene. After addition of the virus, cell plates were centrifuged at 2,000 rpm for 90 min at 32 °C two consecutive days. The cells were incubated for 72 hours from the first infection, they were subculture from passage 1 to 2. After four days in culture (passage 2) cells were trypsinized and sorted in 100 µL of Lysis/Binding Buffer, vortexed and stored at -80 °C until further processing.
processed data file: MusMusculus_Counts.txt
Sox9_CultivatedFBs_LV_4.fastq.gz


title: Empty LV Cultivated Fibroblasts 1

description:
Empty_CultivatedFBs_LV_1
3' RNA-seq
PolyA RNA
Primary mouse cardiac fibroblasts; Mouse cardiac interstitial cells (CIC) from healthy or infarcted 8-10 week old mice heart were obtained by enzymatic digestion. Erythrocytes were removed using RBC lysis buffer and CIC pellet was resuspended in complete medium (DMEM + 10% FBS + 1% P/S + 1% L-Glu) containing 10 ng/mL of bFGF
processed data file: MusMusculus_Counts.txt
Empty_CultivatedFBs_LV_1.fastq.gz

value: Empty Lentivirus


title: Runx1 LV Cultivated Fibroblasts 5

description:
Runx1_CultivatedFBs_LV_5
3' RNA-seq
PolyA RNA
Primary mouse cardiac fibroblasts; Mouse cardiac interstitial cells (CIC) from healthy or infarcted 8-10 week old mice heart were obtained by enzymatic digestion. Erythrocytes were removed using RBC lysis buffer and CIC pellet was resuspended in complete medium (DMEM + 10% FBS + 1% P/S + 1% L-Glu) containing 10 ng/mL of bFGF. For Transcription factors in vitro functional assays, lentiviral transduction was performed in passage 1 CF in cultured medium supplemented with 8 µg/mL polybrene. After addition of the virus, cell plates were centrifuged at 2,000 rpm for 90 min at 32 °C two consecutive days. The cells were incubated for 72 hours from the first infection, they were subculture from passage 1 to 2. After four days in culture (passage 2) cells were trypsinized and sorted in 100 µL of Lysis/Binding Buffer, vortexed and stored at -80 °C until further processing.
processed data file: MusMusculus_Counts.txt
Runx1_CultivatedFBs_LV_5.fastq.gz


title: Runx1 LV Cultivated Fibroblasts 1

description:
Runx1_CultivatedFBs_LV_1
3' RNA-seq
PolyA RNA
Primary mouse cardiac fibroblasts; Mouse cardiac interstitial cells (CIC) from healthy or infarcted 8-10 week old mice heart were obtained by enzymatic digestion. Erythrocytes were removed using RBC lysis buffer and CIC pellet was resuspended in complete medium (DMEM + 10% FBS + 1% P/S + 1% L-Glu) containing 10 ng/mL of bFGF. For Transcription factors in vitro functional assays, lentiviral transduction was performed in passage 1 CF in cultured medium supplemented with 8 µg/mL polybrene. After addition of the virus, cell plates were centrifuged at 2,000 rpm for 90 min at 32 °C two consecutive days. The cells were incubated for 72 hours from the first infection, they were subculture from passage 1 to 2. After four days in culture (passage 2) cells were trypsinized and sorted in 100 µL of Lysis/Binding Buffer, vortexed and stored at -80 °C until further processing.
processed data file: MusMusculus_Counts.txt
Runx1_CultivatedFBs_LV_1.fastq.gz


title: Control LV Cultivated Fibroblasts 1

description:
Control_CultivatedFBs_LV_1
3' RNA-seq
PolyA RNA
Primary mouse cardiac fibroblasts; Mouse cardiac interstitial cells (CIC) from healthy or infarcted 8-10 week old mice heart were obtained by enzymatic digestion. Erythrocytes were removed using RBC lysis buffer and CIC pellet was resuspended in complete medium (DMEM + 10% FBS + 1% P/S + 1% L-Glu) containing 10 ng/mL of bFGF
processed data file: MusMusculus_Counts.txt
Control_CultivatedFBs_LV_1.fastq.gz

value: Control for Lentivirus


title: Empty LV Cultivated Fibroblasts 6

description:
Empty_CultivatedFBs_LV_6
3' RNA-seq
PolyA RNA
Primary mouse cardiac fibroblasts; Mouse cardiac interstitial cells (CIC) from healthy or infarcted 8-10 week old mice heart were obtained by enzymatic digestion. Erythrocytes were removed using RBC lysis buffer and CIC pellet was resuspended in complete medium (DMEM + 10% FBS + 1% P/S + 1% L-Glu) containing 10 ng/mL of bFGF
processed data file: MusMusculus_Counts.txt
Empty_CultivatedFBs_LV_6.fastq.gz


title: 7dpi Cd200 Positive Cd146 Negative 1

description:
7dpi_Cd200Pos_Cd146Neg_1
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
7dpi_Cd200Pos_Cd146Neg_1.fastq.gz

value: Cd200+ Cd146- cells


title: 7dpi GFP Positive Infarct Zone 1

description:
7dpi_GFP_InfarctZone_1
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
7dpi_GFP_InfarctZone_1.fastq.gz

value: Infarct Zone


title: 7dpi GFP Positive Infarct Zone 2

description:
7dpi_GFP_InfarctZone_2
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
7dpi_GFP_InfarctZone_2.fastq.gz


title: Empty LV Cultivated Fibroblasts 5

description:
Empty_CultivatedFBs_LV_5
3' RNA-seq
PolyA RNA
Primary mouse cardiac fibroblasts; Mouse cardiac interstitial cells (CIC) from healthy or infarcted 8-10 week old mice heart were obtained by enzymatic digestion. Erythrocytes were removed using RBC lysis buffer and CIC pellet was resuspended in complete medium (DMEM + 10% FBS + 1% P/S + 1% L-Glu) containing 10 ng/mL of bFGF
processed data file: MusMusculus_Counts.txt
Empty_CultivatedFBs_LV_5.fastq.gz


title: Control LV Cultivated Fibroblasts 3

description:
Control_CultivatedFBs_LV_3
3' RNA-seq
PolyA RNA
Primary mouse cardiac fibroblasts; Mouse cardiac interstitial cells (CIC) from healthy or infarcted 8-10 week old mice heart were obtained by enzymatic digestion. Erythrocytes were removed using RBC lysis buffer and CIC pellet was resuspended in complete medium (DMEM + 10% FBS + 1% P/S + 1% L-Glu) containing 10 ng/mL of bFGF
processed data file: MusMusculus_Counts.txt
Control_CultivatedFBs_LV_3.fastq.gz


title: Control LV Cultivated Fibroblasts 2

description:
Control_CultivatedFBs_LV_2
3' RNA-seq
PolyA RNA
Primary mouse cardiac fibroblasts; Mouse cardiac interstitial cells (CIC) from healthy or infarcted 8-10 week old mice heart were obtained by enzymatic digestion. Erythrocytes were removed using RBC lysis buffer and CIC pellet was resuspended in complete medium (DMEM + 10% FBS + 1% P/S + 1% L-Glu) containing 10 ng/mL of bFGF
processed data file: MusMusculus_Counts.txt
Control_CultivatedFBs_LV_2.fastq.gz


title: Empty LV Cultivated Fibroblasts 4

description:
Empty_CultivatedFBs_LV_4
3' RNA-seq
PolyA RNA
Primary mouse cardiac fibroblasts; Mouse cardiac interstitial cells (CIC) from healthy or infarcted 8-10 week old mice heart were obtained by enzymatic digestion. Erythrocytes were removed using RBC lysis buffer and CIC pellet was resuspended in complete medium (DMEM + 10% FBS + 1% P/S + 1% L-Glu) containing 10 ng/mL of bFGF
processed data file: MusMusculus_Counts.txt
Empty_CultivatedFBs_LV_4.fastq.gz


title: Empty LV Cultivated Fibroblasts 2

description:
Empty_CultivatedFBs_LV_2
3' RNA-seq
PolyA RNA
Primary mouse cardiac fibroblasts; Mouse cardiac interstitial cells (CIC) from healthy or infarcted 8-10 week old mice heart were obtained by enzymatic digestion. Erythrocytes were removed using RBC lysis buffer and CIC pellet was resuspended in complete medium (DMEM + 10% FBS + 1% P/S + 1% L-Glu) containing 10 ng/mL of bFGF
processed data file: MusMusculus_Counts.txt
Empty_CultivatedFBs_LV_2.fastq.gz


title: 7dpi GFP Positive Border Zone 1

description:
7dpi_GFP_BorderZone_1
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
7dpi_GFP_BorderZone_1.fastq.gz

value: Border Zone


title: 7dpi GFP Positive Border Zone 2

description:
7dpi_GFP_BorderZone_2
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
7dpi_GFP_BorderZone_2.fastq.gz


title: 30dpi Dermal Fibroblasts 1

description:
30dpi_Dermal_1
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
30dpi_Dermal_1.fastq.gz

source_name: Dermal fibroblasts

value: Dermal Fibroblasts


title: 7dpi GFP Positive Remote Zone 1

description:
7dpi_GFP_RemoteZone_1
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
7dpi_GFP_RemoteZone_1.fastq.gz

value: Remote Zone


title: Healthy Dermal Fibroblasts 1

description:
Healthy_Dermal_1
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
Healthy_Dermal_1.fastq.gz

value: Healthy


title: 7dpi Cd200 Positive Cd146 Negative 2

description:
7dpi_Cd200Pos_Cd146Neg_2
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
7dpi_Cd200Pos_Cd146Neg_2.fastq.gz


title: 7dpi Cd200 Negative Cd146 Negative 1

description:
7dpi_Cd200Neg_Cd146Neg_1
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
7dpi_Cd200Neg_Cd146Neg_1.fastq.gz

value: Cd200- Cd146- cells


title: 7dpi CD45 Positive 4

description:
7dpi_CD45_4
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
7dpi_CD45_4.fastq.gz

value: Bone Marrow-Derived


title: 7dpi CD45 Positive 3

description:
7dpi_CD45_3
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
7dpi_CD45_3.fastq.gz


title: 7dpi Cd200 Negative Cd146 Negative 2

description:
7dpi_Cd200Neg_Cd146Neg_2
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
7dpi_Cd200Neg_Cd146Neg_2.fastq.gz


title: Healthy CD45 Positive 2

description:
Healthy_CD45_2
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
Healthy_CD45_2.fastq.gz


title: Empty LV Cultivated Fibroblasts 3

description:
Empty_CultivatedFBs_LV_3
3' RNA-seq
PolyA RNA
Primary mouse cardiac fibroblasts; Mouse cardiac interstitial cells (CIC) from healthy or infarcted 8-10 week old mice heart were obtained by enzymatic digestion. Erythrocytes were removed using RBC lysis buffer and CIC pellet was resuspended in complete medium (DMEM + 10% FBS + 1% P/S + 1% L-Glu) containing 10 ng/mL of bFGF
processed data file: MusMusculus_Counts.txt
Empty_CultivatedFBs_LV_3.fastq.gz

value: Cultivated

value: Cultivated Cardiac Fibroblasts


title: 7dpi GFP Positive Remote Zone 2

description:
7dpi_GFP_RemoteZone_2
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
7dpi_GFP_RemoteZone_2.fastq.gz

value: Col1a1-GFP+ cells


title: 30dpi Dermal Fibroblasts 2

description:
30dpi_Dermal_2
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
30dpi_Dermal_2.fastq.gz


title: Healthy Dermal Fibroblasts 2

description:
Healthy_Dermal_2
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
Healthy_Dermal_2.fastq.gz


title: 30dpi CD45 Positive 3

description:
30dpi_CD45_3
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
30dpi_CD45_3.fastq.gz


title: Healthy CD45 Positive 1

description:
Healthy_CD45_1
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
Healthy_CD45_1.fastq.gz


title: 14dpi CD45 Positive 1

description:
14dpi_CD45_1
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
14dpi_CD45_1.fastq.gz


title: 7dpi CD45 Positive 2

description:
7dpi_CD45_2
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
7dpi_CD45_2.fastq.gz


title: 30dpi CD45 Positive 1

description:
30dpi_CD45_1
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
30dpi_CD45_1.fastq.gz


title: 14dpi CD31 Positive 2

description:
14dpi_CD31_2
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
14dpi_CD31_2.fastq.gz


title: Runx1 LV Cultivated Fibroblasts 3

description:
Runx1_CultivatedFBs_LV_3
3' RNA-seq
PolyA RNA
Primary mouse cardiac fibroblasts; Mouse cardiac interstitial cells (CIC) from healthy or infarcted 8-10 week old mice heart were obtained by enzymatic digestion. Erythrocytes were removed using RBC lysis buffer and CIC pellet was resuspended in complete medium (DMEM + 10% FBS + 1% P/S + 1% L-Glu) containing 10 ng/mL of bFGF. For Transcription factors in vitro functional assays, lentiviral transduction was performed in passage 1 CF in cultured medium supplemented with 8 µg/mL polybrene. After addition of the virus, cell plates were centrifuged at 2,000 rpm for 90 min at 32 °C two consecutive days. The cells were incubated for 72 hours from the first infection, they were subculture from passage 1 to 2. After four days in culture (passage 2) cells were trypsinized and sorted in 100 µL of Lysis/Binding Buffer, vortexed and stored at -80 °C until further processing.
processed data file: MusMusculus_Counts.txt
Runx1_CultivatedFBs_LV_3.fastq.gz


title: 14dpi CD31 Positive 1

description:
14dpi_CD31_1
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
14dpi_CD31_1.fastq.gz


title: 30dpi CD45 Positive 2

description:
30dpi_CD45_2
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
30dpi_CD45_2.fastq.gz


title: 7dpi CD31 Positive 3

description:
7dpi_CD31_3
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
7dpi_CD31_3.fastq.gz


title: Healthy CD31 Positive 3

description:
Healthy_CD31_3
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
Healthy_CD31_3.fastq.gz


title: Healthy CD31 Positive 1

description:
Healthy_CD31_1
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
Healthy_CD31_1.fastq.gz


title: 7dpi CD31 Positive 4

description:
7dpi_CD31_4
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
7dpi_CD31_4.fastq.gz


title: Healthy CD31 Positive 4

description:
Healthy_CD31_4
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
Healthy_CD31_4.fastq.gz


title: 14dpi CD45 Positive 2

description:
14dpi_CD45_2
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
14dpi_CD45_2.fastq.gz


title: Healthy CD31 Positive 2

description:
Healthy_CD31_2
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
Healthy_CD31_2.fastq.gz


title: 7dpi CD31 Positive 1

description:
7dpi_CD31_1
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
7dpi_CD31_1.fastq.gz


title: 7dpi GFP Positive 4

description:
7dpi_GFP_4
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
7dpi_GFP_4.fastq.gz


title: Healthy GFP Positive 3

description:
Healthy_GFP_3
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
Healthy_GFP_3.fastq.gz


title: 30dpi CD31 Positive 1

description:
30dpi_CD31_1
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
30dpi_CD31_1.fastq.gz


title: 30dpi CD31 Positive 2

description:
30dpi_CD31_2
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
30dpi_CD31_2.fastq.gz


title: 7dpi GFP Positive 3

description:
7dpi_GFP_3
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
7dpi_GFP_3.fastq.gz


title: Healthy GFP Positive 4

description:
Healthy_GFP_4
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
Healthy_GFP_4.fastq.gz


title: 14dpi GFP Positive 3

description:
14dpi_GFP_3
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
14dpi_GFP_3.fastq.gz


title: 7dpi CD45 Positive 1

description:
7dpi_CD45_1
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
7dpi_CD45_1.fastq.gz


title: 30dpi GFP Positive 2

description:
30dpi_GFP_2
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
30dpi_GFP_2.fastq.gz


title: 7dpi GFP Positive 1

description:
7dpi_GFP_1
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
7dpi_GFP_1.fastq.gz


title: 30dpi CD31 Positive 4

description:
30dpi_CD31_4
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
30dpi_CD31_4.fastq.gz


title: 14dpi GFP Positive 2

description:
14dpi_GFP_2
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
14dpi_GFP_2.fastq.gz


title: 30dpi CD31 Positive 3

description:
30dpi_CD31_3
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
30dpi_CD31_3.fastq.gz


title: 14dpi GFP Positive 1

description:
14dpi_GFP_1
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
14dpi_GFP_1.fastq.gz


title: Healthy GFP Positive 2

description:
Healthy_GFP_2
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
Healthy_GFP_2.fastq.gz


title: 7dpi CD31 Positive 2

description:
7dpi_CD31_2
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
7dpi_CD31_2.fastq.gz


title: Healthy GFP Positive 1

description:
Healthy_GFP_1
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
Healthy_GFP_1.fastq.gz


title: 14dpi GFP Positive 4

description:
14dpi_GFP_4
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
14dpi_GFP_4.fastq.gz


title: DCM Patient Left Ventricle 5

description:
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
HomoSapiens_Counts.txt
HTX42_LV_1

data_processing:
bcl2fastq was used to demultiplex .bcl files and retrieve fastq files according to the sample barcodes
Fastq files were aligned to the corresponding genome (mm10,GRCh38, Sscrofa 11.1) using STAR (v 2.6.1)
Gene level quantification was performed using Rsubread and ensembl transcriptomes (GRCm38.91, Sscrofa11.1.93, and GRCh38.92)
Normalization, processing and differential expression analyses were performed using DEseq2
Genome_build: mm10,GRCh38, Sscrofa 11.1
Supplementary_files_format_and_content: .txt files with raw counts after gene level quantification

source_name: Cardiac Tissue

growth_protocol: primary cell isolates from reporter mice

value: Dilated Cardiomyopathy

value: Cardiac cells

tag: disease

value: Human DCM Sample


title: DCM Patient Right Ventricle 4

description:
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
HomoSapiens_Counts.txt
HTX31_RV_1


title: DCM Patient Left Ventricle 4

description:
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
HomoSapiens_Counts.txt
HTX31_LV_1


title: DCM Patient Right Ventricle 3

description:
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
HomoSapiens_Counts.txt
HTX14_RV_1


title: DCM Patient Left Ventricle 2

description:
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
HomoSapiens_Counts.txt
HTX12_LV_1


title: DCM Patient Right Ventricle 5

description:
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
HomoSapiens_Counts.txt
HTX42_RV_1


title: DCM Patient Left Ventricle 3

description:
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
HomoSapiens_Counts.txt
HTX14_LV_1


title: DCM Patient Left Ventricle 1

description:
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
HomoSapiens_Counts.txt
HTX03_LV_1


title: DCM Patient Right Ventricle 2

description:
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
HomoSapiens_Counts.txt
HTX12_RV_1


title: 7dpi GFP Positive 2

description:
7dpi_GFP_2
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
7dpi_GFP_2.fastq.gz


title: Healthy Right Ventricle 6

description:
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
HomoSapiens_Counts.txt
HD14_RV_1

value: Human Healthy Sample


title: 30dpi GFP Positive 1

description:
30dpi_GFP_1
3' RNA-seq
PolyA RNA
processed data file: MusMusculus_Counts.txt
30dpi_GFP_1.fastq.gz


title: Healthy Left Ventricle 6

description:
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
HomoSapiens_Counts.txt
HD14_LV_1


title: Healthy Left Ventricle 4

description:
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
HomoSapiens_Counts.txt
HD06_LV_1


title: Healthy Left Ventricle 5

description:
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
HomoSapiens_Counts.txt
HD08_LV_1


title: Healthy Right Ventricle 3

description:
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
HomoSapiens_Counts.txt
HD04_RV_1


title: Healthy Left Ventricle 2

description:
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
HomoSapiens_Counts.txt
HD03_LV_1


title: Healthy Right Ventricle 2

description:
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
HomoSapiens_Counts.txt
HD03_RV_1


title: MI Patient Right Ventricle 10

description:
HTX45_RV_1
3' RNA-seq
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
processed data file: HomoSapiens_Counts.txt
HTX45_RV_1.fastq.gz

extract_protocol:
Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturers instructions.
Bulk RNA-seq was performed following MARS-seq adapted for bulk RNA-seq with minor modifications. Briefly, poly-A RNA was extracted with Dynabeads Oligo dT (Ambion) and reverse-transcribed with AffinityScript Multiple Temperature Reverse Transcriptase (Agilent) using poly-dT oligos (IDT) carrying a 7-bp index. Up to 8 samples with similar overall RNA content were pooled together and subjected to linear amplification via IVT using HiScribe T7 High Yield RNA Synthesis Kit (New England Biolabs (NEB)). The resulting antisense RNA was fragmented into 250-350 bps fragments with RNA Fragmentation Reagents (Ambion) and dephosphorylated with 1U FastAP (Thermo Scientific) for 15 min at 37 °C. Partial Illumina adaptor sequences were ligated with T4 RNA Ligase 1 (NEB) followed by a second reverse transcription. Full Illumina adaptor sequences and a secondary barcode were added during library amplification with KAPA HiFi DNA Polymerase (Kapa Biosystems). Libraries were quantified using a Qubit 3.0 Fluorometer and their size profiles examined in Agilent’s 4200 TapeStation System. For Col1a1-GFP+ reporter mouse GFP+/CD31-/CD45- cardiac fibroblasts (CF), GFP-/CD31+/CD45- endothelial cells and GFP-/CD31-/CD45+ bone marrow-derived cells were FACS-sorted in Lysis/Binding Buffer (Ambion).

value: Myocardial Infarction

value: Human MI Sample


title: Healthy Left Ventricle 3

description:
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
HomoSapiens_Counts.txt
HD04_LV_1


title: MI Patient Right Ventricle 8

description:
HTX25_RV_1
3' RNA-seq
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
processed data file: HomoSapiens_Counts.txt
HTX25_RV_1.fastq.gz


title: DCM Patient Right Ventricle 1

description:
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
HomoSapiens_Counts.txt
HTX03_RV_1


title: MI Patient Left Ventricle 10

description:
HTX45_LV_1
3' RNA-seq
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
processed data file: HomoSapiens_Counts.txt
HTX45_LV_1.fastq.gz


title: MI Patient Left Ventricle 9

description:
HTX28_LV_1
3' RNA-seq
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
processed data file: HomoSapiens_Counts.txt
HTX28_LV_1.fastq.gz


title: MI Patient Right Ventricle 9

description:
HTX28_RV_1
3' RNA-seq
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
processed data file: HomoSapiens_Counts.txt
HTX28_RV_1.fastq.gz


title: MI Patient Right Ventricle 4

description:
HTX07_RV_1
3' RNA-seq
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
processed data file: HomoSapiens_Counts.txt
HTX07_RV_1.fastq.gz


title: MI Patient Left Ventricle 4

description:
HTX07_LV_1
3' RNA-seq
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
processed data file: HomoSapiens_Counts.txt
HTX07_LV_1.fastq.gz


title: MI Patient Left Ventricle 8

description:
HTX25_LV_1
3' RNA-seq
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
processed data file: HomoSapiens_Counts.txt
HTX25_LV_1.fastq.gz


title: MI Patient Right Ventricle 2

description:
HTX34_RV_1
3' RNA-seq
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
processed data file: HomoSapiens_Counts.txt
HTX34_RV_1.fastq.gz


title: MI Patient Left Ventricle 5

description:
HTX08_LV_1
3' RNA-seq
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
processed data file: HomoSapiens_Counts.txt
HTX08_LV_1.fastq.gz


title: MI Patient Right Ventricle 5

description:
HTX08_RV_1
3' RNA-seq
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
processed data file: HomoSapiens_Counts.txt
HTX08_RV_1.fastq.gz


title: MI Patient Right Ventricle 1

description:
HTX10_RV_1
3' RNA-seq
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
processed data file: HomoSapiens_Counts.txt
HTX10_RV_1.fastq.gz


title: MI Patient Left Ventricle 7

description:
HTX24_LV_1
3' RNA-seq
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
processed data file: HomoSapiens_Counts.txt
HTX24_LV_1.fastq.gz


title: Healthy Right Ventricle

description:
HD2_RV_1
3' RNA-seq
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
processed data file: HomoSapiens_Counts.txt
HD2_RV_1.fastq.gz


title: 60dpi Swine Remote Zone 5

description:
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
SusScrofa_Counts.txt
60dpi_RemoteZone_SusScrofa_5

organism: Sus scrofa

tag: group


title: 60dpi Swine Remote Zone 3

description:
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
SusScrofa_Counts.txt
60dpi_RemoteZone_SusScrofa_3


title: 60dpi Swine Remote Zone 4

description:
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
SusScrofa_Counts.txt
60dpi_RemoteZone_SusScrofa_4


title: MI Patient Right Ventricle 6

description:
HTX18_RV_1
3' RNA-seq
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
processed data file: HomoSapiens_Counts.txt
HTX18_RV_1.fastq.gz


title: Healthy Right Ventricle 5

description:
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
HomoSapiens_Counts.txt
HD08_RV_1


title: MI Patient Left Ventricle 6

description:
HTX18_LV_1
3' RNA-seq
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
processed data file: HomoSapiens_Counts.txt
HTX18_LV_1.fastq.gz


title: Healthy Left Ventricle

description:
HD2_LV_1
3' RNA-seq
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
processed data file: HomoSapiens_Counts.txt
HD2_LV_1.fastq.gz


title: Healthy Right Ventricle 4

description:
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
HomoSapiens_Counts.txt
HD06_RV_1


title: MI Patient Right Ventricle 3

description:
HTX06_RV_1
3' RNA-seq
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
processed data file: HomoSapiens_Counts.txt
HTX06_RV_1.fastq.gz


title: MI Patient Left Ventricle 2

description:
HTX34_LV_1
3' RNA-seq
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
processed data file: HomoSapiens_Counts.txt
HTX34_LV_1.fastq.gz


title: 60dpi Swine Infarct Zone 6

description:
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
SusScrofa_Counts.txt
60dpi_InfarctZone_SusScrofa_6


title: MI Patient Left Ventricle 3

description:
HTX06_LV_1
3' RNA-seq
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
processed data file: HomoSapiens_Counts.txt
HTX06_LV_1.fastq.gz


title: 60dpi Swine Infarct Zone 5

description:
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
SusScrofa_Counts.txt
60dpi_InfarctZone_SusScrofa_5


title: MI Patient Left Ventricle 1

description:
HTX10_LV_1
3' RNA-seq
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
processed data file: HomoSapiens_Counts.txt
HTX10_LV_1.fastq.gz


title: 60dpi Swine Infarct Zone 1

description:
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
SusScrofa_Counts.txt
60dpi_InfarctZone_SusScrofa_1


title: MI Patient Right Ventricle 7

description:
HTX24_RV_1
3' RNA-seq
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
processed data file: HomoSapiens_Counts.txt
HTX24_RV_1.fastq.gz


title: 60dpi Swine Remote Zone 6

description:
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
SusScrofa_Counts.txt
60dpi_RemoteZone_SusScrofa_6


title: Healthy Swine Model 4

description:
Healthy_SusScrofa_4
3' RNA-seq
Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
processed data file: SusScrofa_Counts.txt
Healthy_SusScrofa_4.fastq.gz

value: Healthy Siwine Model


title: 180dpi Swine Remote Zone 7

description:
180dpi_RemoteZone_SusScrofa_7
3' RNA-seq
Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
processed data file: SusScrofa_Counts.txt
180dpi_RemoteZone_SusScrofa_7.fastq.gz


title: 60dpi Swine Remote Zone 2

description:
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
SusScrofa_Counts.txt
60dpi_RemoteZone_SusScrofa_2


title: 60dpi Swine Remote Zone 1

description:
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
SusScrofa_Counts.txt
60dpi_RemoteZone_SusScrofa_1


title: 180dpi Swine Infarct Zone 7

description:
180dpi_InfarctZone_SusScrofa_7
3' RNA-seq
Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
processed data file: SusScrofa_Counts.txt
180dpi_InfarctZone_SusScrofa_7.fastq.gz

value: Infarct Zone


title: 180dpi Swine Remote Zone 6

description:
180dpi_RemoteZone_SusScrofa_6
3' RNA-seq
Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
processed data file: SusScrofa_Counts.txt
180dpi_RemoteZone_SusScrofa_6.fastq.gz


title: 60dpi Swine Infarct Zone 2

description:
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
SusScrofa_Counts.txt
60dpi_InfarctZone_SusScrofa_2


title: 60dpi Swine Infarct Zone 3

description:
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
SusScrofa_Counts.txt
60dpi_InfarctZone_SusScrofa_3


title: 180dpi Swine Infarct Zone 5

description:
180dpi_InfarctZone_SusScrofa_5
3' RNA-seq
Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
processed data file: SusScrofa_Counts.txt
180dpi_InfarctZone_SusScrofa_5.fastq.gz


title: 180dpi Swine Remote Zone 5

description:
180dpi_RemoteZone_SusScrofa_5
3' RNA-seq
Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
processed data file: SusScrofa_Counts.txt
180dpi_RemoteZone_SusScrofa_5.fastq.gz


title: 180dpi Swine Infarct Zone 3

description:
180dpi_InfarctZone_SusScrofa_3
3' RNA-seq
Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
processed data file: SusScrofa_Counts.txt
180dpi_InfarctZone_SusScrofa_3.fastq.gz


title: 180dpi Swine Remote Zone 9

description:
180dpi_RemoteZone_SusScrofa_9
3' RNA-seq
Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
processed data file: SusScrofa_Counts.txt
180dpi_RemoteZone_SusScrofa_9.fastq.gz


title: 60dpi Swine Infarct Zone 4

description:
Heart biopsies from the right and left ventricle of healthy and patients with chronic heart failure were collected for molecular analysis. Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
SusScrofa_Counts.txt
60dpi_InfarctZone_SusScrofa_4


title: 180dpi Swine Infarct Zone 8

description:
180dpi_InfarctZone_SusScrofa_8
3' RNA-seq
Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
processed data file: SusScrofa_Counts.txt
180dpi_InfarctZone_SusScrofa_8.fastq.gz


title: 180dpi Swine Remote Zone 8

description:
180dpi_RemoteZone_SusScrofa_8
3' RNA-seq
Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
processed data file: SusScrofa_Counts.txt
180dpi_RemoteZone_SusScrofa_8.fastq.gz


title: 180dpi Swine Infarct Zone 2

description:
180dpi_InfarctZone_SusScrofa_2
3' RNA-seq
Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
processed data file: SusScrofa_Counts.txt
180dpi_InfarctZone_SusScrofa_2.fastq.gz


title: 180dpi Swine Infarct Zone 9

description:
180dpi_InfarctZone_SusScrofa_9
3' RNA-seq
Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
processed data file: SusScrofa_Counts.txt
180dpi_InfarctZone_SusScrofa_9.fastq.gz


title: 180dpi Swine Remote Zone 4

description:
180dpi_RemoteZone_SusScrofa_4
3' RNA-seq
Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
processed data file: SusScrofa_Counts.txt
180dpi_RemoteZone_SusScrofa_4.fastq.gz


title: 8dpi Swine Infarct Zone 2

description:
8dpi_InfarctZone_SusScrofa_2
3' RNA-seq
Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
processed data file: SusScrofa_Counts.txt
8dpi_InfarctZone_SusScrofa_2.fastq.gz


title: 180dpi Swine Infarct Zone 4

description:
180dpi_InfarctZone_SusScrofa_4
3' RNA-seq
Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
processed data file: SusScrofa_Counts.txt
180dpi_InfarctZone_SusScrofa_4.fastq.gz


title: 8dpi Swine Remote Zone 1

description:
8dpi_RemoteZone_SusScrofa_1
3' RNA-seq
Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
processed data file: SusScrofa_Counts.txt
8dpi_RemoteZone_SusScrofa_1.fastq.gz


title: 180dpi Swine Remote Zone 1

description:
180dpi_RemoteZone_SusScrofa_1
3' RNA-seq
Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
processed data file: SusScrofa_Counts.txt
180dpi_RemoteZone_SusScrofa_1.fastq.gz


title: 180dpi Swine Infarct Zone 1

description:
180dpi_InfarctZone_SusScrofa_1
3' RNA-seq
Total RNA was isolated using TRIzol reagent after mechanical homogenization with an Ultra-turrax according to manufacturer’s instructions. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent’s 4200 TapeStation System.
processed data file: SusScrofa_Counts.txt
180dpi_InfarctZone_SusScrofa_1.fastq.gz